Overview

NexSON is a translation of NeXML to JSON using the BadgerFish conventions. Each NexSON file represents a Phylografter study, though it may contain exactly one or all the trees included in the study. The set of elements used in these files is (currently) limited to nexml, otus, otu, trees, tree, node, and edge - note that there is no current support for data matrices. There is also an associated metadata vocabulary currently used for annotating elements of type nexml, otu, tree, and node.

As of October 2013, discussion of syntax of validation-related annotations is taking place on the api.opentreeoflife.org wikiwhen that discussion stabilizes the content there will be migrated to this page.

BadgerFish

BadgerFish is one of several schemes for rendering XML as JSON. Several sites, including a site that appears to be the original, and several refinements were consulted in developing the mapping appropriate for NeXML.

MetaData

OpenTree's NexSON metadata vocabulary uses the URI prefix http://purl.org/opentree-terms#, which is abbreviated to ot:. The vocabulary consists of a number of predicates, and a set of terms specifying a choice of values for a particular predicate. The predicates and the types of their values are listed in Table I.

Table I. Predicate Vocabulary

Element

Name

Type

Description

Nexml (study)

ot:studyPublicationReference

(long) string

A reference (bibliographic citation string) to the publication describing the associated study

id of the tree marked as a candidate for synthesis; may occur multiple times?

ot:specifiedRoot

string

id of the node tagged as root of the tree. This node should be the same as the node bearing the @root identifier.
If the ot:specifiedRoot property is absent, then the tree should be assumed to be arbitrarily rooted (thus the node
bearing the @root identifier may not necessarily be the biologically correct root.)
Note: phylografter does not write a value for this, but will in the future

otu

ot:ottid (was ottolid)

integer

taxon id from OTT

ot:originalLabel

string

label (name) assigned the otu in uploaded tree

ot:treebaseOTUId

string

Treebase id for otu (for studies from treebase)

tree

ot:branchLengthMode

choice

Table II

ot:inGroupClade

string

id of the node tagged as root of ingroup root (note this node may not have an assigned otu)

ot:tag

string

tag attached to the tree; may indicate deprecation or inference method; may occur multiple times

ot:branchLengthTimeUnit

string

currently phylografter only writes "Myr", which reflects its internal default.
Not meaningful if ot:branchLengthMode is not ot:time